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Detection, delineation, measurement and display of cavities in macromolecular structures
Abstract
A computer program, VOIDOO, is described which can be employed in the study of cavities such as they occur in macromolecular structures (in particular, in proteins). The program can be used to detect unknown cavities or to delineate known cavities, either of which may be connected to the outside of the molecule or molecular assembly under study. Optionally, output files can be requested that contain a description of the shape of the cavity which can be displayed by the crystallographic modelling program O. Additionally, VOIDOO can be used to calculate the volume of a molecule and to create a file containing data pertaining to the surface of the molecule which can also be displayed using O. Examples of the use of VOIDOO are given for P2 myelin protein, cellular retinol-binding protein and cellobiohydrolase II. Finally, operational definitions to discern different types of cavity are introduced and guidelines for assessing the accuracy and improving the comparability of cavity calculations are given.
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Citations
Cited by
Liang, J., Woodward, C., & Edelsbrunner, H. (1998) · Protein Science · doi:10.1002/pro.5560070905 · Cited by 1,057
Crystal structures of a multidrug transporter reveal a functionally rotating mechanism
Murakami, S., Nakashima, R., Yamashita, E., Matsumoto, T., & Yamaguchi, A. (2006) · Nature · doi:10.1038/nature05076 · Cited by 773
A gate–latch–lock mechanism for hormone signalling by abscisic acid receptors
Melcher, K., Ng, L.-M., Zhou, X. E., Soon, F.-F., Xu, Y., Suino-Powell, K. M., Park, S.-Y., Weiner, J. J., Fujii, H., Chinnusamy, V., et al. (2009) · Nature · doi:10.1038/nature08613 · Cited by 731
Barely porous organic cages for hydrogen isotope separation
Liu, M., Zhang, L., Little, M. A., Kapil, V., Ceriotti, M., Yang, S., Ding, L., Holden, D. L., Balderas-Xicohténcatl, R., He, D., et al. (2019) · Science · doi:10.1126/science.aax7427 · Cited by 399
Diversity of properties among catalases
Switala, J., & Loewen, P. C. (2002) · Archives of Biochemistry and Biophysics · doi:10.1016/s0003-9861(02)00049-8 · Cited by 384
Metadata
- Authors
- Kleywegt, G. J., & Jones, T. A.
- Venue
- Acta Crystallographica Section D Biological Crystallography
- Published
- 1994-03-01
- Volume
- 50
- Issue
- 2
- Pages
- 178-185
- ISSN
- 0907-4449 (ISSN-L)
- OpenAlex
- W2103794058
- Cited by
- 969
- References
- 0
- FWCI
- 18.81
- Type
- journal article
- Language
- en
- Open access
- closed
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- Kleywegt, G. J., & Jones, T. A. (1994). Detection, delineation, measurement and display of cavities in macromolecular structures. Acta Crystallographica Section D Biological Crystallography. https://doi.org/10.1107/s0907444993011333
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
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